Dear Kay and Jeff,
frankly, I do not see much justification for any rejection based on
h-cutoff.
French&Wilson only talk about I/sigI cutoff, which also warrants further
scrutiny. It probably could be argued that reflections with I/sigI<-4
are still more likely to be weak than strong so F~0 seems to make more
sense than rejection. The nature of these outliers should probably be
resolved at the integration stage, but these really aren't that
numerous.
As for h>-4 requirement, I don't see French&Wilson even arguing for that
anywhere in the paper. h variable does not reflect any physical
quantity that would come with prior expectation of being non-negative
and while the posterior of the true intensity (for acentric reflections)
is distributed according to the truncated normal distribution N(sigma*h,
sigma^2), I don't really see why h<-4 is "bad".
>From what I understand, Kay has removed h-cutoff from XDSCONV (or never
included it in the first place). Perhaps ctruncate/phenix should change
too? Or am I misunderstanding something and there is some rationale for
h<-4 cutoff?
Cheers,
Ed.
On Wed, 2013-06-19 at 06:47 +0100, Kay Diederichs wrote:
> Hi Jeff,
>
> what I did in XDSCONV is to mitigate the numerical difficulties associated
> with low h (called "Score" in XDSCONV output) values, and I removed the h <
> -4 cutoff. The more negative h becomes, the closer to zero is the resulting
> amplitude, so not applying a h cutoff makes sense (to me, anyway).
> XDSCONV still applies the I < -3*sigma cutoff, by default.
>
> thanks,
>
> Kay
--
I don't know why the sacrifice thing didn't work.
Science behind it seemed so solid.
Julian, King of Lemurs
